Nucleic acid sequences such as DNA and RNA are molecules consisting of four types of bases of adenine (A), cytosine (C), guanine (G) and thymine (T) or uridine (U). It is known that the function of the molecule of the nucleic acid sequence is dependent on the secondary structure of the sequence. The dependency is a nature which is exerted not only by a functional nucleic acid typified by so-called structural gene such as exon, but also by non-structural gene such as intron and by various types of nucleic acid sequence which cannot be internally transcribed in the cell based on the central dogma such as aptamer.
Although the prediction of the secondary structure of the nucleic acid sequence is very important, different structures may be obtained even if the same sequences have each other, and identical or similar structures may be obtained even if the different sequences have each other. In the case that the secondary structure of the nucleic acid sequence has been merely predicted, it can be largely considered that such a structure will not necessarily provide a possibly-suitable secondary structure in such a sequence. Indeed, with regard to an authentically-synthesized nucleic acid sequence such as so-called aptamer, the biological functions are often exerted only from a specific important region of the nucleic acid sequence. It is expected that such specific region(s) has the structural similarity, however, the structural similarities with regard to the other region(s) do not always have each other. Many attempts have been made to improve the accuracy for predicting the secondary structure of the nucleic acid sequence in that a similarity of each secondary structures of the specific nucleic acid sequence is evaluated with the secondary structure of the other nucleic acid sequence.
Examples of the similarity comparison method of the secondary structure of the nucleic acid sequence generally include a method for an evaluation by combining the alignment of the base constituting the nucleic acid sequence with the prediction of the secondary structure of the nucleic acid sequence. In addition, several algorithms have been reported that probabilities for forming base pairs in the nucleic acid sequence is originally estimated, and, based on the probabilities, predicted structure(s) are modified and re-constituted into the actual structure (non-patent related document 1).
However, in the case of evaluating the similarity of the secondary structure of the nucleic acid sequence with such a method, the similarity as overall structure will be basically predicted. Therefore, it is difficult to precisely predict the similarity of the target structure of a nucleic acid sequence which can be taken in the similar structure in localized region not in overall structure.    Non-Patent Related Document 1    Gorodkin et al., Nucleic Acids Research, 1997, vol. 25, p. 3724˜3732